Hi Michael, It is better to have this in 2 commits. That way if you decide in the future that the use of the interpreter object is not ideal and there is a better way to do this, you can revert this commit without losing the bug fix.
Cheers, Edward On 19 May 2010 07:16, <[email protected]> wrote: > Author: michaelbieri > Date: Wed May 19 07:16:47 2010 > New Revision: 11196 > > URL: http://svn.gna.org/viewcvs/relax?rev=11196&view=rev > Log: > relax interpreter is used for generating model-free final run results. > > In addition, spelling mistake of appen to append was corrected. > > Modified: > branches/bieri_gui/gui_bieri/analyses/results_analysis.py > > Modified: branches/bieri_gui/gui_bieri/analyses/results_analysis.py > URL: > http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/analyses/results_analysis.py?rev=11196&r1=11195&r2=11196&view=diff > ============================================================================== > --- branches/bieri_gui/gui_bieri/analyses/results_analysis.py (original) > +++ branches/bieri_gui/gui_bieri/analyses/results_analysis.py Wed May 19 > 07:16:47 2010 > @@ -28,6 +28,7 @@ > import wx.grid > > # relax module imports. > +from prompt.interpreter import Interpreter > from generic_fns.mol_res_spin import spin_loop > > # relax GUI module imports. > @@ -76,12 +77,17 @@ > def model_free_results(self, directory, pdbfile): > """Create the model-free results.""" > > + # Load the interpreter. > + interpreter = Interpreter(show_script=False, quit=False, > raise_relax_error=True) > + interpreter.populate_self() > + interpreter.on(verbose=False) > + > directory = directory + sep + 'final' > > #Read results > pipename = 'Data_extraction ' + str(time.asctime(time.localtime())) > - pipe.create(pipename, 'mf') > - results.read() > + interpreter.pipe.create(pipename, 'mf') > + interpreter.results.read(directory+sep+'results') > > #create a table file and variables for results table > > @@ -96,7 +102,7 @@ > file.write('Data Extraction by relaxGUI, (C) 2009 Michael Bieri') > file.write("\n") > file.write("\n") > - > "self.file.write(""Residue;Model;S2;Rex_[1/s];Te;Relaxation_Parameters\n"")" > + file.write("Residue;Model;S2;Rex [1/s];Te;Relaxation Parameters\n") > file.write("\n") > > #loop over residues > @@ -119,41 +125,41 @@ > > # S2. > if hasattr(spin, 's2'): > - s2 = str(spin.s2) > + s2_value = str(spin.s2) > s2_err = str(spin.s2_err) > if spin.s2 == None: > file.write(";") > - s2.appen('') > - else: > - file.write(";" + s2[0:5]+ " +/- " + s2_err[0:4]) > - s2.appen(s2[0:5]+ " +/- " + s2_err[0:4]) > + s2.append('') > + else: > + file.write(";" + s2_value[0:5]+ " +/- " + s2_err[0:4]) > + s2.append(s2_value[0:5]+ " +/- " + s2_err[0:4]) > > # Rex. > if hasattr(spin, 'rex'): > - rex = str(spin.rex) > + rex_value = str(spin.rex) > rex_err = str(spin.rex_err) > if spin.rex == None: > file.write(";") > - rex.appen('') > - else: > - rex_eff = spin.rex * (int(spin.frq_labels[1]) * 1000000 * 2 > * 3.14159)**2 > - rex = str(rex_eff) > - rex_err_eff = spin.rex_err * (int(spin.frq_labels[1]) * > 1000000 * 2 * 3.14159)**2 > + rex.append('') > + else: > + rex_eff = float(spin.rex) * (int(spin.frq_labels[1]) * > 1000000 * 2 * 3.14159)**2 > + rex_value = str(rex_eff) > + rex_err_eff = float(spin.rex_err) * (int(spin.frq_labels[1]) > * 1000000 * 2 * 3.14159)**2 > rex_err = str(rex_err_eff) > - file.write(";" + rex[0:5]+ " +/- " + rex_err[0:4]) > - rex.appen(rex[0:5]+ " +/- " + rex_err[0:4]) > + file.write(";" + rex_value[0:5]+ " +/- " + rex_err[0:4]) > + rex.append(rex_value[0:5]+ " +/- " + rex_err[0:4]) > > # Te > if hasattr(spin, 'te'): > if spin.te == None: > file.write(";") > - te.appen('') > + te.append('') > else: > te_ps = spin.te * 1e-12 > - te = str(te_ps) > + te_value = str(te_ps) > te_err = str(spin.te_err) > - file.write(";" + te[0:5]+ " +/- " + te_err[0:4]) > - te.appen(te[0:5]+ " +/- " + te_err[0:4]) > + file.write(";" + te_value[0:5]+ " +/- " + te_err[0:4]) > + te.append(te_value[0:5]+ " +/- " + te_err[0:4]) > > # Parameters. > if hasattr(spin, 'params'): > @@ -170,44 +176,44 @@ > > ################################################################################################## > > #Create Single Data Files > - > - value.write(param='rex', file='rex.txt', dir=str(directory) + sep + > 'final_results', force=True) > - value.write(param='s2', file='s2.txt', dir=str(directory) + sep + > 'final_results', force=True) > - value.write(param='s2f', file='s2f.txt', dir=str(directory) + sep + > 'final_results', force=True) > - value.write(param='s2s', file='s2s.txt', dir=str(directory) + sep + > 'final_results', force=True) > - value.write(param='te', file='te.txt', dir=str(directory) + sep + > 'final_results', force=True) > - value.write(param='tf', file='tf.txt', dir=str(directory) + sep + > 'final_results', force=True) > - value.write(param='ts', file='ts.txt', dir=str(directory) + sep + > 'final_results', force=True) > - value.write(param='rex', file='rex.txt', dir=str(directory) + sep + > 'final_results', force=True) > - value.write(param='r', file='r.txt', dir=str(directory) + sep + > 'final_results', force=True) > - value.write(param='rex', file='rex.txt', dir=str(directory) + sep + > 'final_results', force=True) > - value.write(param='csa', file='csa.txt', dir=str(directory) + sep + > 'final_results', force=True) > - value.write(param='rex', file='rex.txt', dir=str(directory) + sep + > 'final_results', force=True) > - value.write(param='local_tm', file='local_tm.txt', dir=str(directory) + > sep + 'final_results', force=True) > + print 'here' > + interpreter.value.write(param='rex', file='rex.txt', dir=str(directory) > + sep + 'final_results', force=True) > + interpreter.value.write(param='s2', file='s2.txt', dir=str(directory) + > sep + 'final_results', force=True) > + interpreter.value.write(param='s2f', file='s2f.txt', dir=str(directory) > + sep + 'final_results', force=True) > + interpreter.value.write(param='s2s', file='s2s.txt', dir=str(directory) > + sep + 'final_results', force=True) > + interpreter.value.write(param='te', file='te.txt', dir=str(directory) + > sep + 'final_results', force=True) > + interpreter.value.write(param='tf', file='tf.txt', dir=str(directory) + > sep + 'final_results', force=True) > + interpreter.value.write(param='ts', file='ts.txt', dir=str(directory) + > sep + 'final_results', force=True) > + interpreter.value.write(param='rex', file='rex.txt', dir=str(directory) > + sep + 'final_results', force=True) > + interpreter.value.write(param='r', file='r.txt', dir=str(directory) + > sep + 'final_results', force=True) > + interpreter.value.write(param='rex', file='rex.txt', dir=str(directory) > + sep + 'final_results', force=True) > + interpreter.value.write(param='csa', file='csa.txt', dir=str(directory) > + sep + 'final_results', force=True) > + interpreter.value.write(param='rex', file='rex.txt', dir=str(directory) > + sep + 'final_results', force=True) > + interpreter.value.write(param='local_tm', file='local_tm.txt', > dir=str(directory) + sep + 'final_results', force=True) > > > ################################################################################################## > > #Create Grace Plots > > - grace.write(x_data_type='spin', y_data_type='s2', file='s2.agr', > dir=str(directory) + sep + 'grace', force=True) > - grace.write(x_data_type='spin', y_data_type='te', file='te.agr', > dir=str(directory) + sep + 'grace', force=True) > - grace.write(x_data_type='spin', y_data_type='s2f', file='s2f.agr', > dir=str(directory) + sep + 'grace', force=True) > - grace.write(x_data_type='spin', y_data_type='s2s', file='s2s.agr', > dir=str(directory) + sep + 'grace', force=True) > - grace.write(x_data_type='spin', y_data_type='ts', file='ts.agr', > dir=str(directory) + sep + 'grace', force=True) > - grace.write(x_data_type='spin', y_data_type='tf', file='tf.agr', > dir=str(directory) + sep + 'grace', force=True) > - grace.write(x_data_type='spin', y_data_type='csa', file='csa.agr', > dir=str(directory) + sep + 'grace', force=True) > - grace.write(x_data_type='te', y_data_type='s2', file='s2-te.agr', > dir=str(directory) + sep + 'grace', force=True) > + interpreter.grace.write(x_data_type='spin', y_data_type='s2', > file='s2.agr', dir=str(directory) + sep + 'grace', force=True) > + interpreter.grace.write(x_data_type='spin', y_data_type='te', > file='te.agr', dir=str(directory) + sep + 'grace', force=True) > + interpreter.grace.write(x_data_type='spin', y_data_type='s2f', > file='s2f.agr', dir=str(directory) + sep + 'grace', force=True) > + interpreter.grace.write(x_data_type='spin', y_data_type='s2s', > file='s2s.agr', dir=str(directory) + sep + 'grace', force=True) > + interpreter.grace.write(x_data_type='spin', y_data_type='ts', > file='ts.agr', dir=str(directory) + sep + 'grace', force=True) > + interpreter.grace.write(x_data_type='spin', y_data_type='tf', > file='tf.agr', dir=str(directory) + sep + 'grace', force=True) > + interpreter.grace.write(x_data_type='spin', y_data_type='csa', > file='csa.agr', dir=str(directory) + sep + 'grace', force=True) > + interpreter.grace.write(x_data_type='te', y_data_type='s2', > file='s2-te.agr', dir=str(directory) + sep + 'grace', force=True) > > > ################################################################################################## > > #Create Diffusion Tensor > > # Display the diffusion tensor. > - diffusion_tensor.display() > + interpreter.diffusion_tensor.display() > > # Create the tensor PDB file. > tensor_file = 'tensor.pdb' > - structure.create_diff_tensor_pdb(file=tensor_file, dir=str(directory) + > sep, force=True) > + interpreter.structure.create_diff_tensor_pdb(file=tensor_file, > dir=str(directory) + sep, force=True) > > # create diffusion tensor macro > file = open(str(directory) + sep + 'diffusion_tensor.pml', 'w') > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-commits mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
